Pathway Analysis for FABIA Ensembles
John Zhuang
2024-06-17
library(multiMiR)## Welcome to multiMiR.
##
## multiMiR database URL has been set to the
## default value: http://multimir.org/
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## Database Version: 2.3.0 Updated: 2020-04-15library(clusterProfiler)## ## clusterProfiler v4.12.2 Learn more at https://yulab-smu.top/contribution-knowledge-mining/
##
## Please cite:
##
## S Xu, E Hu, Y Cai, Z Xie, X Luo, L Zhan, W Tang, Q Wang, B Liu, R Wang,
## W Xie, T Wu, L Xie, G Yu. Using clusterProfiler to characterize
## multiomics data. Nature Protocols. 2024, doi:10.1038/s41596-024-01020-z##
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## filterlibrary(org.Hs.eg.db)## Loading required package: AnnotationDbi## Loading required package: stats4## Loading required package: BiocGenerics##
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## match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
## Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
## tapply, union, unique, unsplit, which.max, which.min## Loading required package: Biobase## Welcome to Bioconductor
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## Vignettes contain introductory material; view with
## 'browseVignettes()'. To cite Bioconductor, see
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## select## library(stringr)
library(ggplot2)0. Loading of Results
A. List of all Gene names in the dataset
gene.names = readRDS("data/derived/unique_gene_names.rds")B. Selected Features
results.superbiclust.fabia20 = readRDS("data/sel_features/results_superbiclust.fabia.rds")
sel.features = results.superbiclust.fabia20$resNames
sel.features## [[1]]
## [1] "hsa-mir-1185-1" "hsa-mir-1185-2" "hsa-mir-1197" "hsa-mir-323"
## [5] "hsa-mir-329-1" "hsa-mir-329-2" "hsa-mir-370" "hsa-mir-376a-1"
## [9] "hsa-mir-377" "hsa-mir-380" "hsa-mir-433" "hsa-mir-487a"
## [13] "hsa-mir-496" "hsa-mir-541" "hsa-mir-654" "hsa-mir-655"
## [17] "hsa-mir-656" "hsa-mir-668" "hsa-mir-770"
##
## [[2]]
## [1] "hsa-mir-1185-1" "hsa-mir-1185-2" "hsa-mir-1197" "hsa-mir-127"
## [5] "hsa-mir-134" "hsa-mir-136" "hsa-mir-154" "hsa-mir-323"
## [9] "hsa-mir-323b" "hsa-mir-329-1" "hsa-mir-329-2" "hsa-mir-370"
## [13] "hsa-mir-376a-1" "hsa-mir-376a-2" "hsa-mir-376c" "hsa-mir-377"
## [17] "hsa-mir-380" "hsa-mir-382" "hsa-mir-409" "hsa-mir-433"
## [21] "hsa-mir-487a" "hsa-mir-487b" "hsa-mir-494" "hsa-mir-496"
## [25] "hsa-mir-539" "hsa-mir-541" "hsa-mir-654" "hsa-mir-655"
## [29] "hsa-mir-656" "hsa-mir-665" "hsa-mir-668" "hsa-mir-770"
## [33] "hsa-mir-889"
##
## [[3]]
## [1] "hsa-mir-506" "hsa-mir-507" "hsa-mir-508" "hsa-mir-509-1"
## [5] "hsa-mir-509-2" "hsa-mir-509-3" "hsa-mir-510" "hsa-mir-513a-1"
## [9] "hsa-mir-513a-2" "hsa-mir-513b" "hsa-mir-513c" "hsa-mir-514-1"
## [13] "hsa-mir-514-2" "hsa-mir-514-3"
##
## [[4]]
## [1] "hsa-mir-1185-1" "hsa-mir-1185-2" "hsa-mir-1197" "hsa-mir-127"
## [5] "hsa-mir-134" "hsa-mir-154" "hsa-mir-299" "hsa-mir-323"
## [9] "hsa-mir-323b" "hsa-mir-329-1" "hsa-mir-329-2" "hsa-mir-370"
## [13] "hsa-mir-376a-1" "hsa-mir-376c" "hsa-mir-377" "hsa-mir-380"
## [17] "hsa-mir-382" "hsa-mir-409" "hsa-mir-411" "hsa-mir-485"
## [21] "hsa-mir-487a" "hsa-mir-494" "hsa-mir-496" "hsa-mir-541"
## [25] "hsa-mir-543" "hsa-mir-654" "hsa-mir-655" "hsa-mir-656"
## [29] "hsa-mir-668" "hsa-mir-770" "hsa-mir-889"
##
## [[5]]
## [1] "hsa-mir-1185-1" "hsa-mir-1185-2" "hsa-mir-329-1" "hsa-mir-329-2"
## [5] "hsa-mir-380" "hsa-mir-487a" "hsa-mir-655" "hsa-mir-656"
## [9] "hsa-mir-665" "hsa-mir-770"
##
## [[6]]
## [1] "hsa-mir-517a" "hsa-mir-518b"
##
## [[7]]
## [1] "hsa-mir-876"
##
## [[8]]
## [1] "hsa-mir-507" "hsa-mir-509-1" "hsa-mir-509-2" "hsa-mir-510"
## [5] "hsa-mir-513a-2"
##
## [[9]]
## [1] "hsa-mir-1185-1" "hsa-mir-380" "hsa-mir-487a" "hsa-mir-655"
## [5] "hsa-mir-656"
##
## [[10]]
## [1] "hsa-mir-507" "hsa-mir-510"
##
## [[11]]
## character(0)
##
## [[12]]
## [1] "FN1.R2Gn"
##
## [[13]]
## [1] "hsa-mir-510"
##
## [[14]]
## [1] "hsa-mir-656"
##
## [[15]]
## character(0)
##
## [[16]]
## [1] "hsa-mir-1185-1" "hsa-mir-1185-2" "hsa-mir-329-1" "hsa-mir-329-2"
## [5] "hsa-mir-370" "hsa-mir-376a-1" "hsa-mir-377" "hsa-mir-380"
## [9] "hsa-mir-411" "hsa-mir-433" "hsa-mir-487a" "hsa-mir-494"
## [13] "hsa-mir-541" "hsa-mir-655" "hsa-mir-656" "hsa-mir-665"
## [17] "hsa-mir-668" "hsa-mir-770"
##
## [[17]]
## character(0)
##
## [[18]]
## [1] "G6PD.RPPA"
##
## [[19]]
## character(0)
##
## [[20]]
## character(0)
##
## [[21]]
## character(0)
##
## [[22]]
## [1] "GAPDH.R2Gn"
##
## [[23]]
## character(0)
##
## [[24]]
## character(0)
##
## [[25]]
## character(0)
##
## [[26]]
## [1] "CTNNB1.R2Gn"
##
## [[27]]
## character(0)
##
## [[28]]
## [1] "TGM2.R2Gn"
##
## [[29]]
## character(0)
##
## [[30]]
## character(0)
##
## [[31]]
## character(0)1. Convert microRNA to genes
Also remove the ending “.R2Gn” and “.RPPA” from gene names.
split.by.omic = function(variable.list) {
out.mRSG = variable.list[startsWith(variable.list, "hsa")]
out.R2Gn = variable.list[endsWith(variable.list, "R2Gn")]
out.RPPA = variable.list[endsWith(variable.list, "RPPA")]
out = list("miRNASeqGene" = out.mRSG,
"RNASeq2GeneNorm" = out.R2Gn,
"RPPAArray" = out.RPPA)
out
}multiomics.to.GENES = function(sel.features, full.search = F, table = "validated", drop.miRNA = F) {
multiomics.list = split.by.omic(sel.features)
# Convert miRNASeqGene to target GENE names
# Skipped and returns an empty list instead of the list of select features,
# or if microRNA features are explicitly dropped (drop.miRNA = T).
# (Usually done when the features has only a few miRNA and unable to target any genes)
if (length(multiomics.list[[1]]) > 0 & !drop.miRNA) {
if (!full.search) { # Search only among the 198 genes in ACC, recommended
targets= get_multimir(mirna = multiomics.list[[1]],
target = gene.names,
table = table,
summary = T)
mRSG.target.genes = unique(targets@data$target_symbol)
} else { # Search the full dataset, not recommended.
# Use only if ACC gene search returns nothing or fails.
# Genes not in the ACC genes need to be manually removed.
targets= get_multimir(mirna = multiomics.list[[1]],
table = table,
summary = T)
mRSG.target.genes = unique(targets@data$target_symbol)
}
} else {
mRSG.target.genes = list()
}
#Remove suffix for Pathway Analysis Compatibility
R2Gn.genes = str_remove(multiomics.list[[2]], ".R2Gn")
RPPA.genes = str_remove(multiomics.list[[3]], ".RPPA")
#Join all cleaned-up genes are remove duplicates.
out1 = c(mRSG.target.genes, R2Gn.genes, RPPA.genes)
out = as.character(unique(out1))
out
}geneNames <- list("biclust1"=multiomics.to.GENES(sel.features[[1]]),
"biclust2"=multiomics.to.GENES(sel.features[[2]]),
"biclust3"=multiomics.to.GENES(sel.features[[3]]),
"biclust4"=multiomics.to.GENES(sel.features[[4]]),
"biclust5"=multiomics.to.GENES(sel.features[[5]]),
#"biclust6"=multiomics.to.GENES(sel.features[[6]], table = "all"), # Only works with table = "all", removed
#"biclust7"=multiomics.to.GENES(sel.features[[7]], full.search = T), #No results found, error
"biclust8"=multiomics.to.GENES(sel.features[[8]]),
#"biclust9"=multiomics.to.GENES(sel.features[[9]], full.search = T), #No results found, error
"biclust10"=multiomics.to.GENES(sel.features[[10]]),
"biclust12"=multiomics.to.GENES(sel.features[[12]]),
#"biclust13"=multiomics.to.GENES(sel.features[[13]], full.search = T), #No results found, error
#"biclust14"=multiomics.to.GENES(sel.features[[14]], full.search = T), #No results found, error
"biclust16"=multiomics.to.GENES(sel.features[[16]]),
"biclust18"=multiomics.to.GENES(sel.features[[18]]),
"biclust22"=multiomics.to.GENES(sel.features[[22]]),
"biclust26"=multiomics.to.GENES(sel.features[[26]]),
"biclust28"=multiomics.to.GENES(sel.features[[28]]))## Searching mirecords ...
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## Searching mirtarbase ...
## Searching tarbase ...geneNames## $biclust1
## [1] "HSPA1A" "AKT1" "VHL" "MTOR" "MAPK8" "CDKN1A" "STAT5A"
##
## $biclust2
## [1] "HSPA1A" "AKT1" "VHL" "MTOR" "MAPK8" "MYH9" "CDKN1A" "FOXO3"
## [9] "ATM" "CASP8" "MACC1" "STAT5A" "CCND1" "YAP1" "MAPK1" "ANLN"
##
## $biclust3
## [1] "ETS1" "XIAP" "MAPK8" "ARID1A" "BID" "NCOA3" "GAB2"
##
## $biclust4
## [1] "HSPA1A" "AKT1" "VHL" "MTOR" "MAPK8" "PTEN" "KRAS" "NRAS"
## [9] "PTK2" "ETS1" "ATM" "CDKN1A" "STAT5A" "ITGA2"
##
## $biclust5
## [1] "MYH9" "CDKN1A" "FOXO3" "ATM" "CASP8" "MACC1" "CCND1" "YAP1"
## [9] "MAPK1" "ANLN"
##
## $biclust8
## [1] "ETS1" "XIAP" "MAPK8" "ARID1A" "BID" "NCOA3" "GAB2"
##
## $biclust10
## [1] "ETS1" "XIAP" "MAPK8" "ARID1A" "BID" "NCOA3" "GAB2"
##
## $biclust12
## [1] "FN1"
##
## $biclust16
## [1] "MYH9" "CDKN1A" "FOXO3" "ATM" "CASP8" "MACC1" "CCND1" "YAP1"
## [9] "MAPK1" "ANLN"
##
## $biclust18
## [1] "G6PD"
##
## $biclust22
## [1] "GAPDH"
##
## $biclust26
## [1] "CTNNB1"
##
## $biclust28
## [1] "TGM2"saveRDS(geneNames, file = "data/sel_features/gene_converted/genes_superbiclust.fabia.rds")2. Pathway Analysis
A. GO Classification
ggo_MF <- list()#functional profile of a geneset for Molecular Function
ggo_BP <- list()#functional profile of a geneset for Biological Process
ggo_CC <- list()#functional profile of a geneset for Cellular Component
for(z in 1:length(geneNames)){
print(z)
input <- geneNames[[z]]
ggo_MF[[z]] <- groupGO(gene=input,
OrgDb = org.Hs.eg.db,
ont="MF",
keyType="SYMBOL",
readable=TRUE)
ggo_BP[[z]] <- groupGO(gene=input,
OrgDb = org.Hs.eg.db,
ont="BP",
keyType="SYMBOL",
readable=TRUE)
ggo_CC[[z]] <- groupGO(gene=input,
OrgDb = org.Hs.eg.db,
ont="CC",
keyType="SYMBOL",
readable=TRUE)
}## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11
## [1] 12
## [1] 13for(z in 1:length(geneNames)) {
print(head(ggo_MF[[z]]))
print(head(ggo_BP[[z]]))
print(head(ggo_CC[[z]]))
}## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/7
## GO:0003824 GO:0003824 catalytic activity 6 6/7
## GO:0005198 GO:0005198 structural molecule activity 0 0/7
## GO:0005215 GO:0005215 transporter activity 0 0/7
## GO:0005488 GO:0005488 binding 7 7/7
## GO:0009055 GO:0009055 electron transfer activity 0 0/7
## geneID
## GO:0003774
## GO:0003824 HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A
## GO:0005198
## GO:0005215
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/STAT5A
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 2 2/7
## GO:0002376 GO:0002376 immune system process 5 5/7
## GO:0008152 GO:0008152 metabolic process 7 7/7
## GO:0009987 GO:0009987 cellular process 7 7/7
## GO:0016032 GO:0016032 viral process 2 2/7
## GO:0022414 GO:0022414 reproductive process 2 2/7
## geneID
## GO:0000003 AKT1/MTOR
## GO:0002376 HSPA1A/AKT1/MTOR/MAPK8/CDKN1A
## GO:0008152 HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/STAT5A
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/STAT5A
## GO:0016032 HSPA1A/AKT1
## GO:0022414 AKT1/MTOR
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 5 5/7
## GO:0044423 GO:0044423 virion component 0 0/7
## GO:0110165 GO:0110165 cellular anatomical entity 7 7/7
## geneID
## GO:0032991 HSPA1A/AKT1/MTOR/CDKN1A/STAT5A
## GO:0044423
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/STAT5A
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/16
## GO:0003824 GO:0003824 catalytic activity 10 10/16
## GO:0005198 GO:0005198 structural molecule activity 0 0/16
## GO:0005215 GO:0005215 transporter activity 0 0/16
## GO:0005488 GO:0005488 binding 16 16/16
## GO:0009055 GO:0009055 electron transfer activity 0 0/16
## geneID
## GO:0003774 MYH9
## GO:0003824 HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/CCND1/MAPK1
## GO:0005198
## GO:0005215
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/STAT5A/CCND1/YAP1/MAPK1/ANLN
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 6 6/16
## GO:0002376 GO:0002376 immune system process 10 10/16
## GO:0008152 GO:0008152 metabolic process 15 15/16
## GO:0009987 GO:0009987 cellular process 16 16/16
## GO:0016032 GO:0016032 viral process 2 2/16
## GO:0022414 GO:0022414 reproductive process 6 6/16
## geneID
## GO:0000003 AKT1/MTOR/MYH9/FOXO3/ATM/CASP8
## GO:0002376 HSPA1A/AKT1/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MAPK1
## GO:0008152 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/STAT5A/CCND1/YAP1/MAPK1
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/STAT5A/CCND1/YAP1/MAPK1/ANLN
## GO:0016032 HSPA1A/AKT1
## GO:0022414 AKT1/MTOR/MYH9/FOXO3/ATM/CASP8
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 11 11/16
## GO:0044423 GO:0044423 virion component 0 0/16
## GO:0110165 GO:0110165 cellular anatomical entity 16 16/16
## geneID
## GO:0032991 HSPA1A/AKT1/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/STAT5A/CCND1/YAP1
## GO:0044423
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/STAT5A/CCND1/YAP1/MAPK1/ANLN
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/7
## GO:0003824 GO:0003824 catalytic activity 3 3/7
## GO:0005198 GO:0005198 structural molecule activity 0 0/7
## GO:0005215 GO:0005215 transporter activity 0 0/7
## GO:0005488 GO:0005488 binding 7 7/7
## GO:0009055 GO:0009055 electron transfer activity 0 0/7
## geneID
## GO:0003774
## GO:0003824 XIAP/MAPK8/NCOA3
## GO:0005198
## GO:0005215
## GO:0005488 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3/GAB2
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 0 0/7
## GO:0002376 GO:0002376 immune system process 6 6/7
## GO:0008152 GO:0008152 metabolic process 6 6/7
## GO:0009987 GO:0009987 cellular process 7 7/7
## GO:0016032 GO:0016032 viral process 0 0/7
## GO:0022414 GO:0022414 reproductive process 0 0/7
## geneID
## GO:0000003
## GO:0002376 ETS1/XIAP/MAPK8/ARID1A/BID/GAB2
## GO:0008152 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3
## GO:0009987 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3/GAB2
## GO:0016032
## GO:0022414
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 3 3/7
## GO:0044423 GO:0044423 virion component 0 0/7
## GO:0110165 GO:0110165 cellular anatomical entity 7 7/7
## geneID
## GO:0032991 ETS1/ARID1A/NCOA3
## GO:0044423
## GO:0110165 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3/GAB2
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/14
## GO:0003824 GO:0003824 catalytic activity 11 11/14
## GO:0005198 GO:0005198 structural molecule activity 0 0/14
## GO:0005215 GO:0005215 transporter activity 0 0/14
## GO:0005488 GO:0005488 binding 14 14/14
## GO:0009055 GO:0009055 electron transfer activity 0 0/14
## geneID
## GO:0003774
## GO:0003824 HSPA1A/AKT1/VHL/MTOR/MAPK8/PTEN/KRAS/NRAS/PTK2/ATM/CDKN1A
## GO:0005198
## GO:0005215
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/PTEN/KRAS/NRAS/PTK2/ETS1/ATM/CDKN1A/STAT5A/ITGA2
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 5 5/14
## GO:0002376 GO:0002376 immune system process 9 9/14
## GO:0008152 GO:0008152 metabolic process 13 13/14
## GO:0009987 GO:0009987 cellular process 14 14/14
## GO:0016032 GO:0016032 viral process 3 3/14
## GO:0022414 GO:0022414 reproductive process 5 5/14
## geneID
## GO:0000003 AKT1/MTOR/PTEN/ATM/ITGA2
## GO:0002376 HSPA1A/AKT1/MTOR/MAPK8/PTK2/ETS1/ATM/CDKN1A/ITGA2
## GO:0008152 HSPA1A/AKT1/VHL/MTOR/MAPK8/PTEN/KRAS/PTK2/ETS1/ATM/CDKN1A/STAT5A/ITGA2
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/PTEN/KRAS/NRAS/PTK2/ETS1/ATM/CDKN1A/STAT5A/ITGA2
## GO:0016032 HSPA1A/AKT1/ITGA2
## GO:0022414 AKT1/MTOR/PTEN/ATM/ITGA2
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 8 8/14
## GO:0044423 GO:0044423 virion component 0 0/14
## GO:0110165 GO:0110165 cellular anatomical entity 14 14/14
## geneID
## GO:0032991 HSPA1A/AKT1/MTOR/ETS1/ATM/CDKN1A/STAT5A/ITGA2
## GO:0044423
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/PTEN/KRAS/NRAS/PTK2/ETS1/ATM/CDKN1A/STAT5A/ITGA2
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/10
## GO:0003824 GO:0003824 catalytic activity 5 5/10
## GO:0005198 GO:0005198 structural molecule activity 0 0/10
## GO:0005215 GO:0005215 transporter activity 0 0/10
## GO:0005488 GO:0005488 binding 10 10/10
## GO:0009055 GO:0009055 electron transfer activity 0 0/10
## geneID
## GO:0003774 MYH9
## GO:0003824 CDKN1A/ATM/CASP8/CCND1/MAPK1
## GO:0005198
## GO:0005215
## GO:0005488 MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/YAP1/MAPK1/ANLN
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 4 4/10
## GO:0002376 GO:0002376 immune system process 6 6/10
## GO:0008152 GO:0008152 metabolic process 9 9/10
## GO:0009987 GO:0009987 cellular process 10 10/10
## GO:0016032 GO:0016032 viral process 0 0/10
## GO:0022414 GO:0022414 reproductive process 4 4/10
## geneID
## GO:0000003 MYH9/FOXO3/ATM/CASP8
## GO:0002376 MYH9/CDKN1A/FOXO3/ATM/CASP8/MAPK1
## GO:0008152 MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/YAP1/MAPK1
## GO:0009987 MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/YAP1/MAPK1/ANLN
## GO:0016032
## GO:0022414 MYH9/FOXO3/ATM/CASP8
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 7 7/10
## GO:0044423 GO:0044423 virion component 0 0/10
## GO:0110165 GO:0110165 cellular anatomical entity 10 10/10
## geneID
## GO:0032991 MYH9/CDKN1A/FOXO3/ATM/CASP8/CCND1/YAP1
## GO:0044423
## GO:0110165 MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/YAP1/MAPK1/ANLN
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/7
## GO:0003824 GO:0003824 catalytic activity 3 3/7
## GO:0005198 GO:0005198 structural molecule activity 0 0/7
## GO:0005215 GO:0005215 transporter activity 0 0/7
## GO:0005488 GO:0005488 binding 7 7/7
## GO:0009055 GO:0009055 electron transfer activity 0 0/7
## geneID
## GO:0003774
## GO:0003824 XIAP/MAPK8/NCOA3
## GO:0005198
## GO:0005215
## GO:0005488 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3/GAB2
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 0 0/7
## GO:0002376 GO:0002376 immune system process 6 6/7
## GO:0008152 GO:0008152 metabolic process 6 6/7
## GO:0009987 GO:0009987 cellular process 7 7/7
## GO:0016032 GO:0016032 viral process 0 0/7
## GO:0022414 GO:0022414 reproductive process 0 0/7
## geneID
## GO:0000003
## GO:0002376 ETS1/XIAP/MAPK8/ARID1A/BID/GAB2
## GO:0008152 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3
## GO:0009987 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3/GAB2
## GO:0016032
## GO:0022414
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 3 3/7
## GO:0044423 GO:0044423 virion component 0 0/7
## GO:0110165 GO:0110165 cellular anatomical entity 7 7/7
## geneID
## GO:0032991 ETS1/ARID1A/NCOA3
## GO:0044423
## GO:0110165 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3/GAB2
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/7
## GO:0003824 GO:0003824 catalytic activity 3 3/7
## GO:0005198 GO:0005198 structural molecule activity 0 0/7
## GO:0005215 GO:0005215 transporter activity 0 0/7
## GO:0005488 GO:0005488 binding 7 7/7
## GO:0009055 GO:0009055 electron transfer activity 0 0/7
## geneID
## GO:0003774
## GO:0003824 XIAP/MAPK8/NCOA3
## GO:0005198
## GO:0005215
## GO:0005488 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3/GAB2
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 0 0/7
## GO:0002376 GO:0002376 immune system process 6 6/7
## GO:0008152 GO:0008152 metabolic process 6 6/7
## GO:0009987 GO:0009987 cellular process 7 7/7
## GO:0016032 GO:0016032 viral process 0 0/7
## GO:0022414 GO:0022414 reproductive process 0 0/7
## geneID
## GO:0000003
## GO:0002376 ETS1/XIAP/MAPK8/ARID1A/BID/GAB2
## GO:0008152 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3
## GO:0009987 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3/GAB2
## GO:0016032
## GO:0022414
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 3 3/7
## GO:0044423 GO:0044423 virion component 0 0/7
## GO:0110165 GO:0110165 cellular anatomical entity 7 7/7
## geneID
## GO:0032991 ETS1/ARID1A/NCOA3
## GO:0044423
## GO:0110165 ETS1/XIAP/MAPK8/ARID1A/BID/NCOA3/GAB2
## ID Description Count GeneRatio geneID
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/1
## GO:0003824 GO:0003824 catalytic activity 0 0/1
## GO:0005198 GO:0005198 structural molecule activity 1 1/1 FN1
## GO:0005215 GO:0005215 transporter activity 0 0/1
## GO:0005488 GO:0005488 binding 1 1/1 FN1
## GO:0009055 GO:0009055 electron transfer activity 0 0/1
## ID Description Count GeneRatio geneID
## GO:0000003 GO:0000003 reproduction 0 0/1
## GO:0002376 GO:0002376 immune system process 1 1/1 FN1
## GO:0008152 GO:0008152 metabolic process 1 1/1 FN1
## GO:0009987 GO:0009987 cellular process 1 1/1 FN1
## GO:0016032 GO:0016032 viral process 0 0/1
## GO:0022414 GO:0022414 reproductive process 0 0/1
## ID Description Count GeneRatio geneID
## GO:0032991 GO:0032991 protein-containing complex 1 1/1 FN1
## GO:0044423 GO:0044423 virion component 0 0/1
## GO:0110165 GO:0110165 cellular anatomical entity 1 1/1 FN1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/10
## GO:0003824 GO:0003824 catalytic activity 5 5/10
## GO:0005198 GO:0005198 structural molecule activity 0 0/10
## GO:0005215 GO:0005215 transporter activity 0 0/10
## GO:0005488 GO:0005488 binding 10 10/10
## GO:0009055 GO:0009055 electron transfer activity 0 0/10
## geneID
## GO:0003774 MYH9
## GO:0003824 CDKN1A/ATM/CASP8/CCND1/MAPK1
## GO:0005198
## GO:0005215
## GO:0005488 MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/YAP1/MAPK1/ANLN
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 4 4/10
## GO:0002376 GO:0002376 immune system process 6 6/10
## GO:0008152 GO:0008152 metabolic process 9 9/10
## GO:0009987 GO:0009987 cellular process 10 10/10
## GO:0016032 GO:0016032 viral process 0 0/10
## GO:0022414 GO:0022414 reproductive process 4 4/10
## geneID
## GO:0000003 MYH9/FOXO3/ATM/CASP8
## GO:0002376 MYH9/CDKN1A/FOXO3/ATM/CASP8/MAPK1
## GO:0008152 MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/YAP1/MAPK1
## GO:0009987 MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/YAP1/MAPK1/ANLN
## GO:0016032
## GO:0022414 MYH9/FOXO3/ATM/CASP8
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 7 7/10
## GO:0044423 GO:0044423 virion component 0 0/10
## GO:0110165 GO:0110165 cellular anatomical entity 10 10/10
## geneID
## GO:0032991 MYH9/CDKN1A/FOXO3/ATM/CASP8/CCND1/YAP1
## GO:0044423
## GO:0110165 MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/CCND1/YAP1/MAPK1/ANLN
## ID Description Count GeneRatio geneID
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/1
## GO:0003824 GO:0003824 catalytic activity 1 1/1 G6PD
## GO:0005198 GO:0005198 structural molecule activity 0 0/1
## GO:0005215 GO:0005215 transporter activity 0 0/1
## GO:0005488 GO:0005488 binding 1 1/1 G6PD
## GO:0009055 GO:0009055 electron transfer activity 0 0/1
## ID Description Count GeneRatio geneID
## GO:0000003 GO:0000003 reproduction 0 0/1
## GO:0002376 GO:0002376 immune system process 1 1/1 G6PD
## GO:0008152 GO:0008152 metabolic process 1 1/1 G6PD
## GO:0009987 GO:0009987 cellular process 1 1/1 G6PD
## GO:0016032 GO:0016032 viral process 0 0/1
## GO:0022414 GO:0022414 reproductive process 0 0/1
## ID Description Count GeneRatio geneID
## GO:0032991 GO:0032991 protein-containing complex 0 0/1
## GO:0044423 GO:0044423 virion component 0 0/1
## GO:0110165 GO:0110165 cellular anatomical entity 1 1/1 G6PD
## ID Description Count GeneRatio geneID
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/1
## GO:0003824 GO:0003824 catalytic activity 1 1/1 GAPDH
## GO:0005198 GO:0005198 structural molecule activity 0 0/1
## GO:0005215 GO:0005215 transporter activity 0 0/1
## GO:0005488 GO:0005488 binding 1 1/1 GAPDH
## GO:0009055 GO:0009055 electron transfer activity 0 0/1
## ID Description Count GeneRatio geneID
## GO:0000003 GO:0000003 reproduction 0 0/1
## GO:0002376 GO:0002376 immune system process 1 1/1 GAPDH
## GO:0008152 GO:0008152 metabolic process 1 1/1 GAPDH
## GO:0009987 GO:0009987 cellular process 1 1/1 GAPDH
## GO:0016032 GO:0016032 viral process 0 0/1
## GO:0022414 GO:0022414 reproductive process 0 0/1
## ID Description Count GeneRatio geneID
## GO:0032991 GO:0032991 protein-containing complex 1 1/1 GAPDH
## GO:0044423 GO:0044423 virion component 0 0/1
## GO:0110165 GO:0110165 cellular anatomical entity 1 1/1 GAPDH
## ID Description Count GeneRatio geneID
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/1
## GO:0003824 GO:0003824 catalytic activity 0 0/1
## GO:0005198 GO:0005198 structural molecule activity 0 0/1
## GO:0005215 GO:0005215 transporter activity 0 0/1
## GO:0005488 GO:0005488 binding 1 1/1 CTNNB1
## GO:0009055 GO:0009055 electron transfer activity 0 0/1
## ID Description Count GeneRatio geneID
## GO:0000003 GO:0000003 reproduction 1 1/1 CTNNB1
## GO:0002376 GO:0002376 immune system process 1 1/1 CTNNB1
## GO:0008152 GO:0008152 metabolic process 1 1/1 CTNNB1
## GO:0009987 GO:0009987 cellular process 1 1/1 CTNNB1
## GO:0016032 GO:0016032 viral process 0 0/1
## GO:0022414 GO:0022414 reproductive process 1 1/1 CTNNB1
## ID Description Count GeneRatio geneID
## GO:0032991 GO:0032991 protein-containing complex 1 1/1 CTNNB1
## GO:0044423 GO:0044423 virion component 0 0/1
## GO:0110165 GO:0110165 cellular anatomical entity 1 1/1 CTNNB1
## ID Description Count GeneRatio geneID
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/1
## GO:0003824 GO:0003824 catalytic activity 1 1/1 TGM2
## GO:0005198 GO:0005198 structural molecule activity 0 0/1
## GO:0005215 GO:0005215 transporter activity 0 0/1
## GO:0005488 GO:0005488 binding 1 1/1 TGM2
## GO:0009055 GO:0009055 electron transfer activity 0 0/1
## ID Description Count GeneRatio geneID
## GO:0000003 GO:0000003 reproduction 0 0/1
## GO:0002376 GO:0002376 immune system process 0 0/1
## GO:0008152 GO:0008152 metabolic process 1 1/1 TGM2
## GO:0009987 GO:0009987 cellular process 1 1/1 TGM2
## GO:0016032 GO:0016032 viral process 0 0/1
## GO:0022414 GO:0022414 reproductive process 0 0/1
## ID Description Count GeneRatio geneID
## GO:0032991 GO:0032991 protein-containing complex 1 1/1 TGM2
## GO:0044423 GO:0044423 virion component 0 0/1
## GO:0110165 GO:0110165 cellular anatomical entity 1 1/1 TGM2barplot(ggo_MF[[1]], title = "graphGO, Molecular Function, bicluster 1")
barplot(ggo_MF[[2]], title = "graphGO, Molecular Function, bicluster 2")
barplot(ggo_MF[[3]], title = "graphGO, Molecular Function, bicluster 3")
barplot(ggo_MF[[4]], title = "graphGO, Molecular Function, bicluster 4")
barplot(ggo_MF[[5]], title = "graphGO, Molecular Function, bicluster 5")
barplot(ggo_MF[[6]], title = "graphGO, Molecular Function, bicluster 8")
barplot(ggo_MF[[7]], title = "graphGO, Molecular Function, bicluster 10")
barplot(ggo_MF[[8]], title = "graphGO, Molecular Function, bicluster 12")
barplot(ggo_MF[[9]], title = "graphGO, Molecular Function, bicluster 16")
barplot(ggo_MF[[10]], title = "graphGO, Molecular Function, bicluster 18")
barplot(ggo_MF[[11]], title = "graphGO, Molecular Function, bicluster 22")
barplot(ggo_MF[[12]], title = "graphGO, Molecular Function, bicluster 26")
barplot(ggo_MF[[13]], title = "graphGO, Molecular Function, bicluster 28")
barplot(ggo_BP[[1]], title = "graphGO, Biological Process, bicluster 1")
barplot(ggo_BP[[2]], title = "graphGO, Biological Process, bicluster 2")
barplot(ggo_BP[[3]], title = "graphGO, Biological Process, bicluster 3")
barplot(ggo_BP[[4]], title = "graphGO, Biological Process, bicluster 4")
barplot(ggo_BP[[5]], title = "graphGO, Biological Process, bicluster 5")
barplot(ggo_BP[[6]], title = "graphGO, Biological Process, bicluster 8")
barplot(ggo_BP[[7]], title = "graphGO, Biological Process, bicluster 10")
barplot(ggo_BP[[8]], title = "graphGO, Biological Process, bicluster 12")
barplot(ggo_BP[[9]], title = "graphGO, Biological Process, bicluster 16")
barplot(ggo_BP[[10]], title = "graphGO, Biological Process, bicluster 18")
barplot(ggo_BP[[11]], title = "graphGO, Biological Process, bicluster 22")
barplot(ggo_BP[[12]], title = "graphGO, Biological Process, bicluster 26")
barplot(ggo_BP[[13]], title = "graphGO, Biological Process, bicluster 28")
barplot(ggo_CC[[1]], title = "graphGO, Cellular Component, bicluster 1")
barplot(ggo_CC[[2]], title = "graphGO, Cellular Component, bicluster 2")
barplot(ggo_CC[[3]], title = "graphGO, Cellular Component, bicluster 3")
barplot(ggo_CC[[4]], title = "graphGO, Cellular Component, bicluster 4")
barplot(ggo_CC[[5]], title = "graphGO, Cellular Component, bicluster 5")
barplot(ggo_CC[[6]], title = "graphGO, Cellular Component, bicluster 8")
barplot(ggo_CC[[7]], title = "graphGO, Cellular Component, bicluster 10")
barplot(ggo_CC[[8]], title = "graphGO, Cellular Component, bicluster 12")
barplot(ggo_CC[[9]], title = "graphGO, Cellular Component, bicluster 16")
barplot(ggo_CC[[10]], title = "graphGO, Cellular Component, bicluster 18")
barplot(ggo_CC[[11]], title = "graphGO, Cellular Component, bicluster 22")
barplot(ggo_CC[[12]], title = "graphGO, Cellular Component, bicluster 26")
barplot(ggo_CC[[13]], title = "graphGO, Cellular Component, bicluster 28")
B. GO Over-Representation
ego_MF <- list()#GO enrichment of a geneset for Molecular Function
ego_BP <- list()#GO enrichment of a geneset for Molecular Function
ego_CC <- list()#GO enrichment of a geneset for Molecular Function
for(z in 1:length(geneNames)){
print(z)
input <- geneNames[[z]]
ego_MF[[z]] <- enrichGO(
gene = input,
OrgDb = org.Hs.eg.db,
ont = "MF",
pAdjustMethod = "BH",
keyType="SYMBOL",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
minGSSize = 2,
readable = TRUE)
ego_BP[[z]] <- enrichGO(
gene = input,
OrgDb = org.Hs.eg.db,
ont = "BP",
pAdjustMethod = "BH",
keyType="SYMBOL",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
minGSSize = 2,
readable = TRUE)
ego_CC[[z]] <- enrichGO(
gene = input,
OrgDb = org.Hs.eg.db,
ont = "CC",
pAdjustMethod = "BH",
keyType="SYMBOL",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
minGSSize = 2,
readable = TRUE)
}## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11
## [1] 12
## [1] 13for(z in 1:length(geneNames)){
print(head(ego_MF[[z]]))
print(head(ego_BP[[z]]))
print(head(ego_CC[[z]]))
}## ID Description
## GO:0030291 GO:0030291 protein serine/threonine kinase inhibitor activity
## GO:0106310 GO:0106310 protein serine kinase activity
## GO:0004860 GO:0004860 protein kinase inhibitor activity
## GO:0019210 GO:0019210 kinase inhibitor activity
## GO:0004674 GO:0004674 protein serine/threonine kinase activity
## GO:0001156 GO:0001156 TFIIIC-class transcription factor complex binding
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0030291 2/7 37/18522 8.102785e-05 0.006199945 0.001506060
## GO:0106310 3/7 363/18522 2.464449e-04 0.006199945 0.001506060
## GO:0004860 2/7 73/18522 3.176644e-04 0.006199945 0.001506060
## GO:0019210 2/7 78/18522 3.626662e-04 0.006199945 0.001506060
## GO:0004674 3/7 427/18522 3.974324e-04 0.006199945 0.001506060
## GO:0001156 1/7 2/18522 7.557355e-04 0.006314766 0.001533951
## geneID Count
## GO:0030291 AKT1/CDKN1A 2
## GO:0106310 AKT1/MTOR/MAPK8 3
## GO:0004860 AKT1/CDKN1A 2
## GO:0019210 AKT1/CDKN1A 2
## GO:0004674 AKT1/MTOR/MAPK8 3
## GO:0001156 MTOR 1
## ID Description GeneRatio
## GO:0009408 GO:0009408 response to heat 4/7
## GO:0009266 GO:0009266 response to temperature stimulus 4/7
## GO:0034198 GO:0034198 cellular response to amino acid starvation 3/7
## GO:1990928 GO:1990928 response to amino acid starvation 3/7
## GO:0034605 GO:0034605 cellular response to heat 3/7
## GO:0032091 GO:0032091 negative regulation of protein binding 3/7
## BgRatio pvalue p.adjust qvalue
## GO:0009408 104/18888 2.997255e-08 3.380904e-05 7.982164e-06
## GO:0009266 172/18888 2.275196e-07 1.283210e-04 3.029602e-05
## GO:0034198 51/18888 6.441709e-07 2.162617e-04 5.105843e-05
## GO:1990928 54/18888 7.668854e-07 2.162617e-04 5.105843e-05
## GO:0034605 67/18888 1.478057e-06 3.313185e-04 7.822283e-05
## GO:0032091 71/18888 1.762333e-06 3.313185e-04 7.822283e-05
## geneID Count
## GO:0009408 HSPA1A/AKT1/MTOR/CDKN1A 4
## GO:0009266 HSPA1A/AKT1/MTOR/CDKN1A 4
## GO:0034198 MTOR/MAPK8/CDKN1A 3
## GO:1990928 MTOR/MAPK8/CDKN1A 3
## GO:0034605 HSPA1A/MTOR/CDKN1A 3
## GO:0032091 AKT1/MAPK8/CDKN1A 3
## ID Description GeneRatio BgRatio pvalue
## GO:0070557 GO:0070557 PCNA-p21 complex 1/7 2/19894 0.0007036236
## GO:0031931 GO:0031931 TORC1 complex 1/7 6/19894 0.0021095979
## GO:0097441 GO:0097441 basal dendrite 1/7 6/19894 0.0021095979
## GO:0031932 GO:0031932 TORC2 complex 1/7 9/19894 0.0031629656
## GO:0038201 GO:0038201 TOR complex 1/7 12/19894 0.0042153801
## p.adjust qvalue geneID Count
## GO:0070557 0.02531518 0.01628462 CDKN1A 1
## GO:0031931 0.02531518 0.01628462 MTOR 1
## GO:0097441 0.02531518 0.01628462 MAPK8 1
## GO:0031932 0.02846669 0.01831191 MTOR 1
## GO:0038201 0.03035074 0.01952387 MTOR 1
## ID Description
## GO:0106310 GO:0106310 protein serine kinase activity
## GO:0004674 GO:0004674 protein serine/threonine kinase activity
## GO:0004707 GO:0004707 MAP kinase activity
## GO:0070064 GO:0070064 proline-rich region binding
## GO:0042826 GO:0042826 histone deacetylase binding
## GO:0030291 GO:0030291 protein serine/threonine kinase inhibitor activity
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0106310 5/16 363/18522 1.028418e-05 0.001244385 0.0004330180
## GO:0004674 5/16 427/18522 2.252414e-05 0.001362710 0.0004741923
## GO:0004707 2/16 16/18522 8.336346e-05 0.002856537 0.0009940104
## GO:0070064 2/16 17/18522 9.443099e-05 0.002856537 0.0009940104
## GO:0042826 3/16 128/18522 1.690349e-04 0.004090645 0.0014234520
## GO:0030291 2/16 37/18522 4.577980e-04 0.009232259 0.0032126172
## geneID Count
## GO:0106310 AKT1/MTOR/MAPK8/ATM/MAPK1 5
## GO:0004674 AKT1/MTOR/MAPK8/ATM/MAPK1 5
## GO:0004707 MAPK8/MAPK1 2
## GO:0070064 CCND1/YAP1 2
## GO:0042826 HSPA1A/MAPK8/CCND1 3
## GO:0030291 AKT1/CDKN1A 2
## ID Description GeneRatio
## GO:0062197 GO:0062197 cellular response to chemical stress 7/16
## GO:0009408 GO:0009408 response to heat 5/16
## GO:0034599 GO:0034599 cellular response to oxidative stress 6/16
## GO:0034198 GO:0034198 cellular response to amino acid starvation 4/16
## GO:1990928 GO:1990928 response to amino acid starvation 4/16
## GO:0034614 GO:0034614 cellular response to reactive oxygen species 5/16
## BgRatio pvalue p.adjust qvalue
## GO:0062197 311/18888 3.090160e-09 5.185288e-06 1.876866e-06
## GO:0009408 104/18888 1.911902e-08 1.604086e-05 5.806146e-06
## GO:0034599 248/18888 3.459920e-08 1.935249e-05 7.004821e-06
## GO:0034198 51/18888 8.376414e-08 3.337785e-05 1.208144e-05
## GO:1990928 54/18888 1.058426e-07 3.337785e-05 1.208144e-05
## GO:0034614 151/18888 1.243248e-07 3.337785e-05 1.208144e-05
## geneID Count
## GO:0062197 HSPA1A/AKT1/MTOR/MAPK8/FOXO3/ATM/MAPK1 7
## GO:0009408 HSPA1A/AKT1/MTOR/CDKN1A/ATM 5
## GO:0034599 HSPA1A/AKT1/MAPK8/FOXO3/ATM/MAPK1 6
## GO:0034198 MTOR/MAPK8/CDKN1A/MAPK1 4
## GO:1990928 MTOR/MAPK8/CDKN1A/MAPK1 4
## GO:0034614 AKT1/MAPK8/FOXO3/ATM/MAPK1 5
## ID Description
## GO:0005826 GO:0005826 actomyosin contractile ring
## GO:0070938 GO:0070938 contractile ring
## GO:0005819 GO:0005819 spindle
## GO:0008180 GO:0008180 COP9 signalosome
## GO:0005741 GO:0005741 mitochondrial outer membrane
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0005826 2/16 4/19894 3.635235e-06 0.0003635235 0.0001913281
## GO:0070938 2/16 10/19894 2.718760e-05 0.0013593802 0.0007154633
## GO:0005819 4/16 433/19894 3.272457e-04 0.0094003057 0.0049475293
## GO:0008180 2/16 36/19894 3.760122e-04 0.0094003057 0.0049475293
## GO:0005741 3/16 219/19894 6.628567e-04 0.0121604395 0.0064002313
## GO:0000307 2/16 56/19894 9.105620e-04 0.0121604395 0.0064002313
## geneID Count
## GO:0005826 MYH9/ANLN 2
## GO:0070938 MYH9/ANLN 2
## GO:0005819 AKT1/MYH9/ATM/MAPK1 4
## GO:0008180 HSPA1A/MYH9 2
## GO:0005741 MTOR/FOXO3/CASP8 3
## GO:0000307 CDKN1A/CCND1 2
## ID
## GO:0120283 GO:0120283
## GO:0003713 GO:0003713
## GO:0030374 GO:0030374
## GO:0061629 GO:0061629
## GO:0140297 GO:0140297
## GO:0016922 GO:0016922
## Description
## GO:0120283 protein serine/threonine kinase binding
## GO:0003713 transcription coactivator activity
## GO:0030374 nuclear receptor coactivator activity
## GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding
## GO:0140297 DNA-binding transcription factor binding
## GO:0016922 nuclear receptor binding
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0120283 2/7 7/18522 2.568771e-06 0.0001592638 6.489527e-05
## GO:0003713 3/7 271/18522 1.038059e-04 0.0032179819 1.311232e-03
## GO:0030374 2/7 55/18522 1.800853e-04 0.0032316692 1.316809e-03
## GO:0061629 3/7 343/18522 2.084948e-04 0.0032316692 1.316809e-03
## GO:0140297 3/7 478/18522 5.532853e-04 0.0068607374 2.795547e-03
## GO:0016922 2/7 136/18522 1.097114e-03 0.0100388592 4.090537e-03
## geneID Count
## GO:0120283 XIAP/MAPK8 2
## GO:0003713 ETS1/ARID1A/NCOA3 3
## GO:0030374 ETS1/NCOA3 2
## GO:0061629 ETS1/ARID1A/NCOA3 3
## GO:0140297 ETS1/ARID1A/NCOA3 3
## GO:0016922 ARID1A/NCOA3 2
## ID
## GO:1902459 GO:1902459
## GO:0030522 GO:0030522
## GO:2000036 GO:2000036
## GO:0039531 GO:0039531
## GO:1902528 GO:1902528
## GO:1902530 GO:1902530
## Description
## GO:1902459 positive regulation of stem cell population maintenance
## GO:0030522 intracellular receptor signaling pathway
## GO:2000036 regulation of stem cell population maintenance
## GO:0039531 regulation of cytoplasmic pattern recognition receptor signaling pathway
## GO:1902528 regulation of protein linear polyubiquitination
## GO:1902530 positive regulation of protein linear polyubiquitination
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:1902459 2/7 48/18888 0.0001317291 0.04033235 0.01854731
## GO:0030522 3/7 369/18888 0.0002441855 0.04033235 0.01854731
## GO:2000036 2/7 73/18888 0.0003055481 0.04033235 0.01854731
## GO:0039531 2/7 108/18888 0.0006676434 0.04192472 0.01927958
## GO:1902528 1/7 2/18888 0.0007410936 0.04192472 0.01927958
## GO:1902530 1/7 2/18888 0.0007410936 0.04192472 0.01927958
## geneID Count
## GO:1902459 ARID1A/NCOA3 2
## GO:0030522 XIAP/MAPK8/ARID1A 3
## GO:2000036 ARID1A/NCOA3 2
## GO:0039531 XIAP/MAPK8 2
## GO:1902528 XIAP 1
## GO:1902530 XIAP 1
## ID Description GeneRatio BgRatio pvalue p.adjust
## GO:0097441 GO:0097441 basal dendrite 1/7 6/19894 0.002109598 0.01460451
## GO:0140092 GO:0140092 bBAF complex 1/7 10/19894 0.003513876 0.01460451
## GO:0035060 GO:0035060 brahma complex 1/7 14/19894 0.004916460 0.01460451
## GO:0071564 GO:0071564 npBAF complex 1/7 14/19894 0.004916460 0.01460451
## GO:0071565 GO:0071565 nBAF complex 1/7 16/19894 0.005617118 0.01460451
## GO:0016514 GO:0016514 SWI/SNF complex 1/7 30/19894 0.010509889 0.02277143
## qvalue geneID Count
## GO:0097441 0.007095307 MAPK8 1
## GO:0140092 0.007095307 ARID1A 1
## GO:0035060 0.007095307 ARID1A 1
## GO:0071564 0.007095307 ARID1A 1
## GO:0071565 0.007095307 ARID1A 1
## GO:0016514 0.011063041 ARID1A 1
## ID Description
## GO:0106310 GO:0106310 protein serine kinase activity
## GO:0004674 GO:0004674 protein serine/threonine kinase activity
## GO:0030291 GO:0030291 protein serine/threonine kinase inhibitor activity
## GO:0003925 GO:0003925 G protein activity
## GO:0004860 GO:0004860 protein kinase inhibitor activity
## GO:0019003 GO:0019003 GDP binding
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0106310 4/14 363/18522 0.0001243240 0.01398998 0.004044545
## GO:0004674 4/14 427/18522 0.0002320529 0.01398998 0.004044545
## GO:0030291 2/14 37/18522 0.0003480386 0.01398998 0.004044545
## GO:0003925 2/14 45/18522 0.0005155705 0.01398998 0.004044545
## GO:0004860 2/14 73/18522 0.0013521609 0.01398998 0.004044545
## GO:0019003 2/14 75/18522 0.0014265635 0.01398998 0.004044545
## geneID Count
## GO:0106310 AKT1/MTOR/MAPK8/ATM 4
## GO:0004674 AKT1/MTOR/MAPK8/ATM 4
## GO:0030291 AKT1/CDKN1A 2
## GO:0003925 KRAS/NRAS 2
## GO:0004860 AKT1/CDKN1A 2
## GO:0019003 KRAS/NRAS 2
## ID Description
## GO:0010632 GO:0010632 regulation of epithelial cell migration
## GO:0010634 GO:0010634 positive regulation of epithelial cell migration
## GO:0010631 GO:0010631 epithelial cell migration
## GO:0090132 GO:0090132 epithelium migration
## GO:0090130 GO:0090130 tissue migration
## GO:0009408 GO:0009408 response to heat
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0010632 7/14 298/18888 7.082024e-10 1.117543e-06 3.682652e-07
## GO:0010634 6/14 177/18888 1.755369e-09 1.279107e-06 4.215054e-07
## GO:0010631 7/14 375/18888 3.501293e-09 1.279107e-06 4.215054e-07
## GO:0090132 7/14 378/18888 3.700139e-09 1.279107e-06 4.215054e-07
## GO:0090130 7/14 383/18888 4.052937e-09 1.279107e-06 4.215054e-07
## GO:0009408 5/14 104/18888 8.839902e-09 2.324894e-06 7.661248e-07
## geneID Count
## GO:0010632 AKT1/MTOR/PTEN/PTK2/ETS1/STAT5A/ITGA2 7
## GO:0010634 AKT1/MTOR/PTK2/ETS1/STAT5A/ITGA2 6
## GO:0010631 AKT1/MTOR/PTEN/PTK2/ETS1/STAT5A/ITGA2 7
## GO:0090132 AKT1/MTOR/PTEN/PTK2/ETS1/STAT5A/ITGA2 7
## GO:0090130 AKT1/MTOR/PTEN/PTK2/ETS1/STAT5A/ITGA2 7
## GO:0009408 HSPA1A/AKT1/MTOR/ATM/CDKN1A 5
## ID Description GeneRatio BgRatio
## GO:0005925 GO:0005925 focal adhesion 4/14 421/19894
## GO:0030055 GO:0030055 cell-substrate junction 4/14 431/19894
## GO:0070557 GO:0070557 PCNA-p21 complex 1/14 2/19894
## GO:0034666 GO:0034666 integrin alpha2-beta1 complex 1/14 3/19894
## GO:0016605 GO:0016605 PML body 2/14 108/19894
## GO:0031931 GO:0031931 TORC1 complex 1/14 6/19894
## pvalue p.adjust qvalue geneID Count
## GO:0005925 0.0001672496 0.006680633 0.003949617 HSPA1A/KRAS/PTK2/ITGA2 4
## GO:0030055 0.0001830310 0.006680633 0.003949617 HSPA1A/KRAS/PTK2/ITGA2 4
## GO:0070557 0.0014069997 0.034236992 0.020241048 CDKN1A 1
## GO:0034666 0.0021098099 0.035870172 0.021206591 ITGA2 1
## GO:0016605 0.0025463690 0.035870172 0.021206591 MTOR/PTEN 2
## GO:0031931 0.0042154859 0.035870172 0.021206591 MTOR 1
## ID
## GO:0070064 GO:0070064
## GO:0016538 GO:0016538
## GO:0004677 GO:0004677
## GO:0035979 GO:0035979
## GO:0030295 GO:0030295
## GO:0034246 GO:0034246
## Description
## GO:0070064 proline-rich region binding
## GO:0016538 cyclin-dependent protein serine/threonine kinase regulator activity
## GO:0004677 DNA-dependent protein kinase activity
## GO:0035979 histone H2AXS139 kinase activity
## GO:0030295 protein kinase activator activity
## GO:0034246 mitochondrial transcription factor activity
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0070064 2/10 17/18522 3.552653e-05 0.002415804 0.0007479269
## GO:0016538 2/10 50/18522 3.169725e-04 0.010777065 0.0033365527
## GO:0004677 1/10 3/18522 1.618909e-03 0.017762122 0.0054991088
## GO:0035979 1/10 3/18522 1.618909e-03 0.017762122 0.0054991088
## GO:0030295 2/10 129/18522 2.088189e-03 0.017762122 0.0054991088
## GO:0034246 1/10 4/18522 2.158020e-03 0.017762122 0.0054991088
## geneID Count
## GO:0070064 CCND1/YAP1 2
## GO:0016538 CDKN1A/CCND1 2
## GO:0004677 ATM 1
## GO:0035979 ATM 1
## GO:0030295 CDKN1A/CCND1 2
## GO:0034246 FOXO3 1
## ID Description GeneRatio
## GO:0071480 GO:0071480 cellular response to gamma radiation 3/10
## GO:0031571 GO:0031571 mitotic G1 DNA damage checkpoint signaling 3/10
## GO:0044819 GO:0044819 mitotic G1/S transition checkpoint signaling 3/10
## GO:0001701 GO:0001701 in utero embryonic development 5/10
## GO:0042770 GO:0042770 signal transduction in response to DNA damage 4/10
## GO:0010332 GO:0010332 response to gamma radiation 3/10
## BgRatio pvalue p.adjust qvalue
## GO:0071480 27/18888 3.105065e-07 0.0001393819 4.729419e-05
## GO:0031571 30/18888 4.306340e-07 0.0001393819 4.729419e-05
## GO:0044819 30/18888 4.306340e-07 0.0001393819 4.729419e-05
## GO:0001701 401/18888 9.711876e-07 0.0002357558 7.999519e-05
## GO:0042770 188/18888 1.905112e-06 0.0003699728 1.255369e-04
## GO:0010332 52/18888 2.329784e-06 0.0003770367 1.279338e-04
## geneID Count
## GO:0071480 CDKN1A/ATM/YAP1 3
## GO:0031571 CDKN1A/ATM/CCND1 3
## GO:0044819 CDKN1A/ATM/CCND1 3
## GO:0001701 MYH9/CDKN1A/CASP8/YAP1/MAPK1 5
## GO:0042770 CDKN1A/FOXO3/ATM/CCND1 4
## GO:0010332 CDKN1A/ATM/YAP1 3
## ID Description
## GO:0005826 GO:0005826 actomyosin contractile ring
## GO:0070938 GO:0070938 contractile ring
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:0030864 GO:0030864 cortical actin cytoskeleton
## GO:0032153 GO:0032153 cell division site
## GO:0017053 GO:0017053 transcription repressor complex
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0005826 2/10 4/19894 1.363762e-06 0.0001131922 4.880831e-05
## GO:0070938 2/10 10/19894 1.021177e-05 0.0004237884 1.827369e-04
## GO:0000307 2/10 56/19894 3.451847e-04 0.0090216453 3.890120e-03
## GO:0030864 2/10 72/19894 5.704635e-04 0.0090216453 3.890120e-03
## GO:0032153 2/10 73/19894 5.863756e-04 0.0090216453 3.890120e-03
## GO:0017053 2/10 77/19894 6.521671e-04 0.0090216453 3.890120e-03
## geneID Count
## GO:0005826 MYH9/ANLN 2
## GO:0070938 MYH9/ANLN 2
## GO:0000307 CDKN1A/CCND1 2
## GO:0030864 MYH9/ANLN 2
## GO:0032153 MYH9/ANLN 2
## GO:0017053 FOXO3/CCND1 2
## ID
## GO:0120283 GO:0120283
## GO:0003713 GO:0003713
## GO:0030374 GO:0030374
## GO:0061629 GO:0061629
## GO:0140297 GO:0140297
## GO:0016922 GO:0016922
## Description
## GO:0120283 protein serine/threonine kinase binding
## GO:0003713 transcription coactivator activity
## GO:0030374 nuclear receptor coactivator activity
## GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding
## GO:0140297 DNA-binding transcription factor binding
## GO:0016922 nuclear receptor binding
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0120283 2/7 7/18522 2.568771e-06 0.0001592638 6.489527e-05
## GO:0003713 3/7 271/18522 1.038059e-04 0.0032179819 1.311232e-03
## GO:0030374 2/7 55/18522 1.800853e-04 0.0032316692 1.316809e-03
## GO:0061629 3/7 343/18522 2.084948e-04 0.0032316692 1.316809e-03
## GO:0140297 3/7 478/18522 5.532853e-04 0.0068607374 2.795547e-03
## GO:0016922 2/7 136/18522 1.097114e-03 0.0100388592 4.090537e-03
## geneID Count
## GO:0120283 XIAP/MAPK8 2
## GO:0003713 ETS1/ARID1A/NCOA3 3
## GO:0030374 ETS1/NCOA3 2
## GO:0061629 ETS1/ARID1A/NCOA3 3
## GO:0140297 ETS1/ARID1A/NCOA3 3
## GO:0016922 ARID1A/NCOA3 2
## ID
## GO:1902459 GO:1902459
## GO:0030522 GO:0030522
## GO:2000036 GO:2000036
## GO:0039531 GO:0039531
## GO:1902528 GO:1902528
## GO:1902530 GO:1902530
## Description
## GO:1902459 positive regulation of stem cell population maintenance
## GO:0030522 intracellular receptor signaling pathway
## GO:2000036 regulation of stem cell population maintenance
## GO:0039531 regulation of cytoplasmic pattern recognition receptor signaling pathway
## GO:1902528 regulation of protein linear polyubiquitination
## GO:1902530 positive regulation of protein linear polyubiquitination
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:1902459 2/7 48/18888 0.0001317291 0.04033235 0.01854731
## GO:0030522 3/7 369/18888 0.0002441855 0.04033235 0.01854731
## GO:2000036 2/7 73/18888 0.0003055481 0.04033235 0.01854731
## GO:0039531 2/7 108/18888 0.0006676434 0.04192472 0.01927958
## GO:1902528 1/7 2/18888 0.0007410936 0.04192472 0.01927958
## GO:1902530 1/7 2/18888 0.0007410936 0.04192472 0.01927958
## geneID Count
## GO:1902459 ARID1A/NCOA3 2
## GO:0030522 XIAP/MAPK8/ARID1A 3
## GO:2000036 ARID1A/NCOA3 2
## GO:0039531 XIAP/MAPK8 2
## GO:1902528 XIAP 1
## GO:1902530 XIAP 1
## ID Description GeneRatio BgRatio pvalue p.adjust
## GO:0097441 GO:0097441 basal dendrite 1/7 6/19894 0.002109598 0.01460451
## GO:0140092 GO:0140092 bBAF complex 1/7 10/19894 0.003513876 0.01460451
## GO:0035060 GO:0035060 brahma complex 1/7 14/19894 0.004916460 0.01460451
## GO:0071564 GO:0071564 npBAF complex 1/7 14/19894 0.004916460 0.01460451
## GO:0071565 GO:0071565 nBAF complex 1/7 16/19894 0.005617118 0.01460451
## GO:0016514 GO:0016514 SWI/SNF complex 1/7 30/19894 0.010509889 0.02277143
## qvalue geneID Count
## GO:0097441 0.007095307 MAPK8 1
## GO:0140092 0.007095307 ARID1A 1
## GO:0035060 0.007095307 ARID1A 1
## GO:0071564 0.007095307 ARID1A 1
## GO:0071565 0.007095307 ARID1A 1
## GO:0016514 0.011063041 ARID1A 1
## ID
## GO:0120283 GO:0120283
## GO:0003713 GO:0003713
## GO:0030374 GO:0030374
## GO:0061629 GO:0061629
## GO:0140297 GO:0140297
## GO:0016922 GO:0016922
## Description
## GO:0120283 protein serine/threonine kinase binding
## GO:0003713 transcription coactivator activity
## GO:0030374 nuclear receptor coactivator activity
## GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding
## GO:0140297 DNA-binding transcription factor binding
## GO:0016922 nuclear receptor binding
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0120283 2/7 7/18522 2.568771e-06 0.0001592638 6.489527e-05
## GO:0003713 3/7 271/18522 1.038059e-04 0.0032179819 1.311232e-03
## GO:0030374 2/7 55/18522 1.800853e-04 0.0032316692 1.316809e-03
## GO:0061629 3/7 343/18522 2.084948e-04 0.0032316692 1.316809e-03
## GO:0140297 3/7 478/18522 5.532853e-04 0.0068607374 2.795547e-03
## GO:0016922 2/7 136/18522 1.097114e-03 0.0100388592 4.090537e-03
## geneID Count
## GO:0120283 XIAP/MAPK8 2
## GO:0003713 ETS1/ARID1A/NCOA3 3
## GO:0030374 ETS1/NCOA3 2
## GO:0061629 ETS1/ARID1A/NCOA3 3
## GO:0140297 ETS1/ARID1A/NCOA3 3
## GO:0016922 ARID1A/NCOA3 2
## ID
## GO:1902459 GO:1902459
## GO:0030522 GO:0030522
## GO:2000036 GO:2000036
## GO:0039531 GO:0039531
## GO:1902528 GO:1902528
## GO:1902530 GO:1902530
## Description
## GO:1902459 positive regulation of stem cell population maintenance
## GO:0030522 intracellular receptor signaling pathway
## GO:2000036 regulation of stem cell population maintenance
## GO:0039531 regulation of cytoplasmic pattern recognition receptor signaling pathway
## GO:1902528 regulation of protein linear polyubiquitination
## GO:1902530 positive regulation of protein linear polyubiquitination
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:1902459 2/7 48/18888 0.0001317291 0.04033235 0.01854731
## GO:0030522 3/7 369/18888 0.0002441855 0.04033235 0.01854731
## GO:2000036 2/7 73/18888 0.0003055481 0.04033235 0.01854731
## GO:0039531 2/7 108/18888 0.0006676434 0.04192472 0.01927958
## GO:1902528 1/7 2/18888 0.0007410936 0.04192472 0.01927958
## GO:1902530 1/7 2/18888 0.0007410936 0.04192472 0.01927958
## geneID Count
## GO:1902459 ARID1A/NCOA3 2
## GO:0030522 XIAP/MAPK8/ARID1A 3
## GO:2000036 ARID1A/NCOA3 2
## GO:0039531 XIAP/MAPK8 2
## GO:1902528 XIAP 1
## GO:1902530 XIAP 1
## ID Description GeneRatio BgRatio pvalue p.adjust
## GO:0097441 GO:0097441 basal dendrite 1/7 6/19894 0.002109598 0.01460451
## GO:0140092 GO:0140092 bBAF complex 1/7 10/19894 0.003513876 0.01460451
## GO:0035060 GO:0035060 brahma complex 1/7 14/19894 0.004916460 0.01460451
## GO:0071564 GO:0071564 npBAF complex 1/7 14/19894 0.004916460 0.01460451
## GO:0071565 GO:0071565 nBAF complex 1/7 16/19894 0.005617118 0.01460451
## GO:0016514 GO:0016514 SWI/SNF complex 1/7 30/19894 0.010509889 0.02277143
## qvalue geneID Count
## GO:0097441 0.007095307 MAPK8 1
## GO:0140092 0.007095307 ARID1A 1
## GO:0035060 0.007095307 ARID1A 1
## GO:0071564 0.007095307 ARID1A 1
## GO:0071565 0.007095307 ARID1A 1
## GO:0016514 0.011063041 ARID1A 1
## ID Description GeneRatio
## GO:0043394 GO:0043394 proteoglycan binding 1/1
## GO:0016504 GO:0016504 peptidase activator activity 1/1
## GO:0005518 GO:0005518 collagen binding 1/1
## GO:0002020 GO:0002020 protease binding 1/1
## GO:0005178 GO:0005178 integrin binding 1/1
## GO:0005201 GO:0005201 extracellular matrix structural constituent 1/1
## BgRatio pvalue p.adjust qvalue geneID Count
## GO:0043394 36/18522 0.001943635 0.01223770 NA FN1 1
## GO:0016504 55/18522 0.002969442 0.01223770 NA FN1 1
## GO:0005518 68/18522 0.003671310 0.01223770 NA FN1 1
## GO:0002020 140/18522 0.007558579 0.01342033 NA FN1 1
## GO:0005178 157/18522 0.008476406 0.01342033 NA FN1 1
## GO:0005201 166/18522 0.008962315 0.01342033 NA FN1 1
## ID
## GO:1904235 GO:1904235
## GO:1904237 GO:1904237
## GO:0006931 GO:0006931
## GO:0150102 GO:0150102
## GO:0007161 GO:0007161
## GO:1901166 GO:1901166
## Description
## GO:1904235 regulation of substrate-dependent cell migration, cell attachment to substrate
## GO:1904237 positive regulation of substrate-dependent cell migration, cell attachment to substrate
## GO:0006931 substrate-dependent cell migration, cell attachment to substrate
## GO:0150102 negative regulation of monocyte activation
## GO:0007161 calcium-independent cell-matrix adhesion
## GO:1901166 neural crest cell migration involved in autonomic nervous system development
## GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
## GO:1904235 1/1 2/18888 0.0001058873 0.003256036 NA FN1 1
## GO:1904237 1/1 2/18888 0.0001058873 0.003256036 NA FN1 1
## GO:0006931 1/1 3/18888 0.0001588310 0.003256036 NA FN1 1
## GO:0150102 1/1 3/18888 0.0001588310 0.003256036 NA FN1 1
## GO:0007161 1/1 4/18888 0.0002117747 0.003473105 NA FN1 1
## GO:1901166 1/1 6/18888 0.0003176620 0.004341381 NA FN1 1
## ID Description
## GO:0005577 GO:0005577 fibrinogen complex
## GO:0031093 GO:0031093 platelet alpha granule lumen
## GO:0031091 GO:0031091 platelet alpha granule
## GO:0005604 GO:0005604 basement membrane
## GO:0005793 GO:0005793 endoplasmic reticulum-Golgi intermediate compartment
## GO:0072562 GO:0072562 blood microparticle
## GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
## GO:0005577 1/1 8/19894 0.0004021313 0.005227707 NA FN1 1
## GO:0031093 1/1 67/19894 0.0033678496 0.015029657 NA FN1 1
## GO:0031091 1/1 91/19894 0.0045742435 0.015029657 NA FN1 1
## GO:0005604 1/1 92/19894 0.0046245099 0.015029657 NA FN1 1
## GO:0005793 1/1 133/19894 0.0066854328 0.015683121 NA FN1 1
## GO:0072562 1/1 144/19894 0.0072383633 0.015683121 NA FN1 1
## ID
## GO:0070064 GO:0070064
## GO:0016538 GO:0016538
## GO:0004677 GO:0004677
## GO:0035979 GO:0035979
## GO:0030295 GO:0030295
## GO:0034246 GO:0034246
## Description
## GO:0070064 proline-rich region binding
## GO:0016538 cyclin-dependent protein serine/threonine kinase regulator activity
## GO:0004677 DNA-dependent protein kinase activity
## GO:0035979 histone H2AXS139 kinase activity
## GO:0030295 protein kinase activator activity
## GO:0034246 mitochondrial transcription factor activity
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0070064 2/10 17/18522 3.552653e-05 0.002415804 0.0007479269
## GO:0016538 2/10 50/18522 3.169725e-04 0.010777065 0.0033365527
## GO:0004677 1/10 3/18522 1.618909e-03 0.017762122 0.0054991088
## GO:0035979 1/10 3/18522 1.618909e-03 0.017762122 0.0054991088
## GO:0030295 2/10 129/18522 2.088189e-03 0.017762122 0.0054991088
## GO:0034246 1/10 4/18522 2.158020e-03 0.017762122 0.0054991088
## geneID Count
## GO:0070064 CCND1/YAP1 2
## GO:0016538 CDKN1A/CCND1 2
## GO:0004677 ATM 1
## GO:0035979 ATM 1
## GO:0030295 CDKN1A/CCND1 2
## GO:0034246 FOXO3 1
## ID Description GeneRatio
## GO:0071480 GO:0071480 cellular response to gamma radiation 3/10
## GO:0031571 GO:0031571 mitotic G1 DNA damage checkpoint signaling 3/10
## GO:0044819 GO:0044819 mitotic G1/S transition checkpoint signaling 3/10
## GO:0001701 GO:0001701 in utero embryonic development 5/10
## GO:0042770 GO:0042770 signal transduction in response to DNA damage 4/10
## GO:0010332 GO:0010332 response to gamma radiation 3/10
## BgRatio pvalue p.adjust qvalue
## GO:0071480 27/18888 3.105065e-07 0.0001393819 4.729419e-05
## GO:0031571 30/18888 4.306340e-07 0.0001393819 4.729419e-05
## GO:0044819 30/18888 4.306340e-07 0.0001393819 4.729419e-05
## GO:0001701 401/18888 9.711876e-07 0.0002357558 7.999519e-05
## GO:0042770 188/18888 1.905112e-06 0.0003699728 1.255369e-04
## GO:0010332 52/18888 2.329784e-06 0.0003770367 1.279338e-04
## geneID Count
## GO:0071480 CDKN1A/ATM/YAP1 3
## GO:0031571 CDKN1A/ATM/CCND1 3
## GO:0044819 CDKN1A/ATM/CCND1 3
## GO:0001701 MYH9/CDKN1A/CASP8/YAP1/MAPK1 5
## GO:0042770 CDKN1A/FOXO3/ATM/CCND1 4
## GO:0010332 CDKN1A/ATM/YAP1 3
## ID Description
## GO:0005826 GO:0005826 actomyosin contractile ring
## GO:0070938 GO:0070938 contractile ring
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:0030864 GO:0030864 cortical actin cytoskeleton
## GO:0032153 GO:0032153 cell division site
## GO:0017053 GO:0017053 transcription repressor complex
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0005826 2/10 4/19894 1.363762e-06 0.0001131922 4.880831e-05
## GO:0070938 2/10 10/19894 1.021177e-05 0.0004237884 1.827369e-04
## GO:0000307 2/10 56/19894 3.451847e-04 0.0090216453 3.890120e-03
## GO:0030864 2/10 72/19894 5.704635e-04 0.0090216453 3.890120e-03
## GO:0032153 2/10 73/19894 5.863756e-04 0.0090216453 3.890120e-03
## GO:0017053 2/10 77/19894 6.521671e-04 0.0090216453 3.890120e-03
## geneID Count
## GO:0005826 MYH9/ANLN 2
## GO:0070938 MYH9/ANLN 2
## GO:0000307 CDKN1A/CCND1 2
## GO:0030864 MYH9/ANLN 2
## GO:0032153 MYH9/ANLN 2
## GO:0017053 FOXO3/CCND1 2
## ID
## GO:0004345 GO:0004345
## GO:0005536 GO:0005536
## GO:0050661 GO:0050661
## GO:0048029 GO:0048029
## GO:0016616 GO:0016616
## GO:0016614 GO:0016614
## Description
## GO:0004345 glucose-6-phosphate dehydrogenase activity
## GO:0005536 glucose binding
## GO:0050661 NADP binding
## GO:0048029 monosaccharide binding
## GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
## GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
## GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
## GO:0004345 1/1 2/18522 0.0001079797 0.0007558579 NA G6PD 1
## GO:0005536 1/1 11/18522 0.0005938883 0.0020786092 NA G6PD 1
## GO:0050661 1/1 53/18522 0.0028614620 0.0066767448 NA G6PD 1
## GO:0048029 1/1 74/18522 0.0039952489 0.0069916856 NA G6PD 1
## GO:0016616 1/1 125/18522 0.0067487312 0.0085034014 NA G6PD 1
## GO:0016614 1/1 135/18522 0.0072886297 0.0085034014 NA G6PD 1
## ID
## GO:0010731 GO:0010731
## GO:0010732 GO:0010732
## GO:0010734 GO:0010734
## GO:0019322 GO:0019322
## GO:1904879 GO:1904879
## GO:0009051 GO:0009051
## Description
## GO:0010731 protein glutathionylation
## GO:0010732 regulation of protein glutathionylation
## GO:0010734 negative regulation of protein glutathionylation
## GO:0019322 pentose biosynthetic process
## GO:1904879 positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel
## GO:0009051 pentose-phosphate shunt, oxidative branch
## GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
## GO:0010731 1/1 2/18888 0.0001058873 0.003388395 NA G6PD 1
## GO:0010732 1/1 2/18888 0.0001058873 0.003388395 NA G6PD 1
## GO:0010734 1/1 2/18888 0.0001058873 0.003388395 NA G6PD 1
## GO:0019322 1/1 2/18888 0.0001058873 0.003388395 NA G6PD 1
## GO:1904879 1/1 3/18888 0.0001588310 0.003872451 NA G6PD 1
## GO:0009051 1/1 4/18888 0.0002117747 0.003872451 NA G6PD 1
## ID Description GeneRatio BgRatio
## GO:0034451 GO:0034451 centriolar satellite 1/1 126/19894
## GO:0009898 GO:0009898 cytoplasmic side of plasma membrane 1/1 161/19894
## GO:0098562 GO:0098562 cytoplasmic side of membrane 1/1 199/19894
## pvalue p.adjust qvalue geneID Count
## GO:0034451 0.006333568 0.01000302 NA G6PD 1
## GO:0009898 0.008092892 0.01000302 NA G6PD 1
## GO:0098562 0.010003016 0.01000302 NA G6PD 1
## ID
## GO:0004365 GO:0004365
## GO:0043891 GO:0043891
## GO:0019828 GO:0019828
## GO:0016769 GO:0016769
## GO:0097718 GO:0097718
## GO:0016620 GO:0016620
## Description
## GO:0004365 glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
## GO:0043891 glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) activity
## GO:0019828 aspartic-type endopeptidase inhibitor activity
## GO:0016769 transferase activity, transferring nitrogenous groups
## GO:0097718 disordered domain specific binding
## GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
## GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
## GO:0004365 1/1 2/18522 0.0001079797 0.0008638376 NA GAPDH 1
## GO:0043891 1/1 2/18522 0.0001079797 0.0008638376 NA GAPDH 1
## GO:0019828 1/1 8/18522 0.0004319188 0.0023035669 NA GAPDH 1
## GO:0016769 1/1 26/18522 0.0014037361 0.0050870436 NA GAPDH 1
## GO:0097718 1/1 32/18522 0.0017276752 0.0050870436 NA GAPDH 1
## GO:0016620 1/1 39/18522 0.0021056041 0.0050870436 NA GAPDH 1
## ID Description GeneRatio
## GO:0035606 GO:0035606 peptidyl-cysteine S-trans-nitrosylation 1/1
## GO:0017014 GO:0017014 protein nitrosylation 1/1
## GO:0018119 GO:0018119 peptidyl-cysteine S-nitrosylation 1/1
## GO:0051873 GO:0051873 killing by host of symbiont cells 1/1
## GO:0018198 GO:0018198 peptidyl-cysteine modification 1/1
## GO:0050832 GO:0050832 defense response to fungus 1/1
## BgRatio pvalue p.adjust qvalue geneID Count
## GO:0035606 2/18888 0.0001058873 0.008259212 NA GAPDH 1
## GO:0017014 16/18888 0.0008470987 0.016071980 NA GAPDH 1
## GO:0018119 16/18888 0.0008470987 0.016071980 NA GAPDH 1
## GO:0051873 28/18888 0.0014824227 0.016071980 NA GAPDH 1
## GO:0018198 45/18888 0.0023824651 0.016071980 NA GAPDH 1
## GO:0050832 56/18888 0.0029648454 0.016071980 NA GAPDH 1
## ID Description GeneRatio BgRatio pvalue
## GO:0097452 GO:0097452 GAIT complex 1/1 4/19894 0.0002010656
## GO:0005811 GO:0005811 lipid droplet 1/1 104/19894 0.0052277068
## GO:0031965 GO:0031965 nuclear membrane 1/1 313/19894 0.0157333870
## GO:0005635 GO:0005635 nuclear envelope 1/1 498/19894 0.0250326732
## p.adjust qvalue geneID Count
## GO:0097452 0.0008042626 NA GAPDH 1
## GO:0005811 0.0104554137 NA GAPDH 1
## GO:0031965 0.0209778493 NA GAPDH 1
## GO:0005635 0.0250326732 NA GAPDH 1
## ID Description GeneRatio BgRatio
## GO:0045294 GO:0045294 alpha-catenin binding 1/1 10/18522
## GO:0070411 GO:0070411 I-SMAD binding 1/1 16/18522
## GO:0097718 GO:0097718 disordered domain specific binding 1/1 32/18522
## GO:0030331 GO:0030331 nuclear estrogen receptor binding 1/1 39/18522
## GO:0001222 GO:0001222 transcription corepressor binding 1/1 47/18522
## GO:0046332 GO:0046332 SMAD binding 1/1 78/18522
## pvalue p.adjust qvalue geneID Count
## GO:0045294 0.0005398985 0.007342620 NA CTNNB1 1
## GO:0070411 0.0008638376 0.007342620 NA CTNNB1 1
## GO:0097718 0.0017276752 0.008627578 NA CTNNB1 1
## GO:0030331 0.0021056041 0.008627578 NA CTNNB1 1
## GO:0001222 0.0025375229 0.008627578 NA CTNNB1 1
## GO:0046332 0.0042112083 0.011931757 NA CTNNB1 1
## ID
## GO:0003340 GO:0003340
## GO:0045976 GO:0045976
## GO:0061047 GO:0061047
## GO:0072053 GO:0072053
## GO:0072054 GO:0072054
## GO:2000017 GO:2000017
## Description
## GO:0003340 negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis
## GO:0045976 negative regulation of mitotic cell cycle, embryonic
## GO:0061047 positive regulation of branching involved in lung morphogenesis
## GO:0072053 renal inner medulla development
## GO:0072054 renal outer medulla development
## GO:2000017 positive regulation of determination of dorsal identity
## GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
## GO:0003340 1/1 2/18888 0.0001058873 0.003925395 NA CTNNB1 1
## GO:0045976 1/1 2/18888 0.0001058873 0.003925395 NA CTNNB1 1
## GO:0061047 1/1 2/18888 0.0001058873 0.003925395 NA CTNNB1 1
## GO:0072053 1/1 2/18888 0.0001058873 0.003925395 NA CTNNB1 1
## GO:0072054 1/1 2/18888 0.0001058873 0.003925395 NA CTNNB1 1
## GO:2000017 1/1 2/18888 0.0001058873 0.003925395 NA CTNNB1 1
## ID Description GeneRatio BgRatio
## GO:0034750 GO:0034750 Scrib-APC-beta-catenin complex 1/1 2/19894
## GO:1990711 GO:1990711 beta-catenin-ICAT complex 1/1 2/19894
## GO:0070369 GO:0070369 beta-catenin-TCF7L2 complex 1/1 3/19894
## GO:0071664 GO:0071664 catenin-TCF7L2 complex 1/1 4/19894
## GO:0005916 GO:0005916 fascia adherens 1/1 9/19894
## GO:0016600 GO:0016600 flotillin complex 1/1 9/19894
## pvalue p.adjust qvalue geneID Count
## GO:0034750 0.0001005328 0.003166784 NA CTNNB1 1
## GO:1990711 0.0001005328 0.003166784 NA CTNNB1 1
## GO:0070369 0.0001507992 0.003166784 NA CTNNB1 1
## GO:0071664 0.0002010656 0.003166784 NA CTNNB1 1
## GO:0005916 0.0004523977 0.004318342 NA CTNNB1 1
## GO:0016600 0.0004523977 0.004318342 NA CTNNB1 1
## ID
## GO:0003810 GO:0003810
## GO:0016811 GO:0016811
## GO:0016410 GO:0016410
## GO:0016810 GO:0016810
## GO:0140993 GO:0140993
## GO:0016747 GO:0016747
## Description
## GO:0003810 protein-glutamine gamma-glutamyltransferase activity
## GO:0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
## GO:0016410 N-acyltransferase activity
## GO:0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
## GO:0140993 histone modifying activity
## GO:0016747 acyltransferase activity, transferring groups other than amino-acyl groups
## GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
## GO:0003810 1/1 9/18522 0.0004859086 0.004859086 NA TGM2 1
## GO:0016811 1/1 72/18522 0.0038872692 0.017096786 NA TGM2 1
## GO:0016410 1/1 95/18522 0.0051290357 0.017096786 NA TGM2 1
## GO:0016810 1/1 134/18522 0.0072346399 0.018086600 NA TGM2 1
## GO:0140993 1/1 207/18522 0.0111758989 0.020336177 NA TGM2 1
## GO:0016747 1/1 226/18522 0.0122017061 0.020336177 NA TGM2 1
## ID
## GO:0018277 GO:0018277
## GO:0060605 GO:0060605
## GO:0060662 GO:0060662
## GO:0032471 GO:0032471
## GO:0071314 GO:0071314
## GO:2000425 GO:2000425
## Description
## GO:0018277 protein deamination
## GO:0060605 tube lumen cavitation
## GO:0060662 salivary gland cavitation
## GO:0032471 negative regulation of endoplasmic reticulum calcium ion concentration
## GO:0071314 cellular response to cocaine
## GO:2000425 regulation of apoptotic cell clearance
## GeneRatio BgRatio pvalue p.adjust qvalue geneID Count
## GO:0018277 1/1 2/18888 0.0001058873 0.004575846 NA TGM2 1
## GO:0060605 1/1 5/18888 0.0002647183 0.004575846 NA TGM2 1
## GO:0060662 1/1 5/18888 0.0002647183 0.004575846 NA TGM2 1
## GO:0032471 1/1 8/18888 0.0004235493 0.004575846 NA TGM2 1
## GO:0071314 1/1 10/18888 0.0005294367 0.004575846 NA TGM2 1
## GO:2000425 1/1 10/18888 0.0005294367 0.004575846 NA TGM2 1
## ID Description GeneRatio
## GO:0000786 GO:0000786 nucleosome 1/1
## GO:0005925 GO:0005925 focal adhesion 1/1
## GO:0062023 GO:0062023 collagen-containing extracellular matrix 1/1
## GO:0030055 GO:0030055 cell-substrate junction 1/1
## BgRatio pvalue p.adjust qvalue geneID Count
## GO:0000786 135/19894 0.006785966 0.02166482 NA TGM2 1
## GO:0005925 421/19894 0.021162159 0.02166482 NA TGM2 1
## GO:0062023 428/19894 0.021514024 0.02166482 NA TGM2 1
## GO:0030055 431/19894 0.021664824 0.02166482 NA TGM2 1barplot(ego_MF[[1]], title = "enrichGO, Molecular Function, bicluster 1")
barplot(ego_MF[[2]], title = "enrichGO, Molecular Function, bicluster 2")
barplot(ego_MF[[3]], title = "enrichGO, Molecular Function, bicluster 3")
barplot(ego_MF[[4]], title = "enrichGO, Molecular Function, bicluster 4")
barplot(ego_MF[[5]], title = "enrichGO, Molecular Function, bicluster 5")
barplot(ego_MF[[6]], title = "enrichGO, Molecular Function, bicluster 8")
barplot(ego_MF[[7]], title = "enrichGO, Molecular Function, bicluster 10")
barplot(ego_MF[[8]], title = "enrichGO, Molecular Function, bicluster 12")
barplot(ego_MF[[9]], title = "enrichGO, Molecular Function, bicluster 16")
barplot(ego_MF[[10]], title = "enrichGO, Molecular Function, bicluster 18")
barplot(ego_MF[[11]], title = "enrichGO, Molecular Function, bicluster 22")
barplot(ego_MF[[12]], title = "enrichGO, Molecular Function, bicluster 26")
barplot(ego_MF[[13]], title = "enrichGO, Molecular Function, bicluster 28")
barplot(ego_BP[[1]], title = "enrichGO, Biological Process, bicluster 1")
barplot(ego_BP[[2]], title = "enrichGO, Biological Process, bicluster 2")
barplot(ego_BP[[3]], title = "enrichGO, Biological Process, bicluster 3")
barplot(ego_BP[[4]], title = "enrichGO, Biological Process, bicluster 4")
barplot(ego_BP[[5]], title = "enrichGO, Biological Process, bicluster 5")
barplot(ego_BP[[6]], title = "enrichGO, Biological Process, bicluster 8")
barplot(ego_BP[[7]], title = "enrichGO, Biological Process, bicluster 10")
barplot(ego_BP[[8]], title = "enrichGO, Biological Process, bicluster 12")
barplot(ego_BP[[9]], title = "enrichGO, Biological Process, bicluster 16")
barplot(ego_BP[[10]], title = "enrichGO, Biological Process, bicluster 18")
barplot(ego_BP[[11]], title = "enrichGO, Biological Process, bicluster 22")
barplot(ego_BP[[12]], title = "enrichGO, Biological Process, bicluster 26")
barplot(ego_BP[[13]], title = "enrichGO, Biological Process, bicluster 28")
barplot(ego_CC[[1]], title = "enrichGO, Cellular Component, bicluster 1")
barplot(ego_CC[[2]], title = "enrichGO, Cellular Component, bicluster 2")
barplot(ego_CC[[3]], title = "enrichGO, Cellular Component, bicluster 3")
barplot(ego_CC[[4]], title = "enrichGO, Cellular Component, bicluster 4")
barplot(ego_CC[[5]], title = "enrichGO, Cellular Component, bicluster 5")
barplot(ego_CC[[6]], title = "enrichGO, Cellular Component, bicluster 8")
barplot(ego_CC[[7]], title = "enrichGO, Cellular Component, bicluster 10")
barplot(ego_CC[[8]], title = "enrichGO, Cellular Component, bicluster 12")
barplot(ego_CC[[9]], title = "enrichGO, Cellular Component, bicluster 16")
barplot(ego_CC[[10]], title = "enrichGO, Cellular Component, bicluster 18")
barplot(ego_CC[[11]], title = "enrichGO, Cellular Component, bicluster 22")
barplot(ego_CC[[12]], title = "enrichGO, Cellular Component, bicluster 26")
barplot(ego_CC[[13]], title = "enrichGO, Cellular Component, bicluster 28")
DAG plots for ego
goplot(ego_MF[[1]]) + labs(title = "enrichGO, Molecular Function, bicluster 1")
goplot(ego_MF[[2]]) + labs(title = "enrichGO, Molecular Function, bicluster 2")
goplot(ego_MF[[3]]) + labs(title = "enrichGO, Molecular Function, bicluster 3")
goplot(ego_MF[[4]]) + labs(title = "enrichGO, Molecular Function, bicluster 4")
goplot(ego_MF[[5]]) + labs(title = "enrichGO, Molecular Function, bicluster 5")
goplot(ego_MF[[6]]) + labs(title = "enrichGO, Molecular Function, bicluster 8")
goplot(ego_MF[[7]]) + labs(title = "enrichGO, Molecular Function, bicluster 10")
goplot(ego_MF[[8]]) + labs(title = "enrichGO, Molecular Function, bicluster 12")
goplot(ego_MF[[9]]) + labs(title = "enrichGO, Molecular Function, bicluster 16")
goplot(ego_MF[[10]]) + labs(title = "enrichGO, Molecular Function, bicluster 18")
goplot(ego_MF[[11]]) + labs(title = "enrichGO, Molecular Function, bicluster 22")
goplot(ego_MF[[12]]) + labs(title = "enrichGO, Molecular Function, bicluster 26")
goplot(ego_MF[[13]]) + labs(title = "enrichGO, Molecular Function, bicluster 28")
goplot(ego_BP[[1]]) + labs(title = "enrichGO, Biological Process, bicluster 1")## Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[2]]) + labs(title = "enrichGO, Biological Process, bicluster 2")
goplot(ego_BP[[3]]) + labs(title = "enrichGO, Biological Process, bicluster 3")## Warning: ggrepel: 15 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[4]]) + labs(title = "enrichGO, Biological Process, bicluster 4")
goplot(ego_BP[[5]]) + labs(title = "enrichGO, Biological Process, bicluster 5")
goplot(ego_BP[[6]]) + labs(title = "enrichGO, Biological Process, bicluster 8")## Warning: ggrepel: 15 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[7]]) + labs(title = "enrichGO, Biological Process, bicluster 10")## Warning: ggrepel: 15 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[8]]) + labs(title = "enrichGO, Biological Process, bicluster 12")## Warning: ggrepel: 15 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[9]]) + labs(title = "enrichGO, Biological Process, bicluster 16")
goplot(ego_BP[[10]]) + labs(title = "enrichGO, Biological Process, bicluster 18")## Warning: ggrepel: 65 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[11]]) + labs(title = "enrichGO, Biological Process, bicluster 22")## Warning: ggrepel: 71 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[12]]) + labs(title = "enrichGO, Biological Process, bicluster 26")## Warning: ggrepel: 78 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[13]]) + labs(title = "enrichGO, Biological Process, bicluster 28")## Warning: ggrepel: 1 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_CC[[1]]) + labs(title = "enrichGO, Cellular Component, bicluster 1")
goplot(ego_CC[[2]]) + labs(title = "enrichGO, Cellular Component, bicluster 2")
goplot(ego_CC[[3]]) + labs(title = "enrichGO, Cellular Component, bicluster 3")
goplot(ego_CC[[4]]) + labs(title = "enrichGO, Cellular Component, bicluster 4")
goplot(ego_CC[[5]]) + labs(title = "enrichGO, Cellular Component, bicluster 5")
goplot(ego_CC[[6]]) + labs(title = "enrichGO, Cellular Component, bicluster 8")
goplot(ego_CC[[7]]) + labs(title = "enrichGO, Cellular Component, bicluster 10")
goplot(ego_CC[[8]]) + labs(title = "enrichGO, Cellular Component, bicluster 12")
goplot(ego_CC[[9]]) + labs(title = "enrichGO, Cellular Component, bicluster 16")
goplot(ego_CC[[10]]) + labs(title = "enrichGO, Cellular Component, bicluster 18")
goplot(ego_CC[[11]]) + labs(title = "enrichGO, Cellular Component, bicluster 22")
goplot(ego_CC[[12]]) + labs(title = "enrichGO, Cellular Component, bicluster 26")
goplot(ego_CC[[13]]) + labs(title = "enrichGO, Cellular Component, bicluster 28")
3. Export Pathway Analysis result to data
pathway = list("ggo_MF" = ggo_MF,
"ggo_BP" = ggo_BP,
"ggo_CC" = ggo_CC,
"ego_MF" = ego_MF,
"ego_BP" = ego_BP,
"ego_CC" = ego_CC)
saveRDS(pathway, file = "data/out_pathway/pathways_superbiclust.fabia.rds")